Mostly Microbes and Infection - by David Ojcius

A single‑patient study shows how repeat‑associated deletion of a blaNDM‑1 resistance module in Klebsiella pneumoniae produced divergent carbapenem phenotypes among otherwise closely related isolates. Stable genomes, a validated 10.5‑kb plasmid deletion, and growth differences highlight how structural plasmid variation can drive clinically relevant heteroresistance.

A study maps age‑related gut microbiome shifts and introduces MicroAge, a microbiome‑based aging clock. It identifies  Bifidobacterium   pseudocatenulatum as a geroprotective species depleted with age. In mice, supplementation restored intestinal balance, reduced systemic inflammaging, improved cognition and motor function, and extended healthspan. Its metabolite  5-aminovaleric acid betaine (5-AVAB)  reproduced many benefits.

Defined human Clostridia consortia 17‑mix and 11‑mix reverse established colitis in multiple murine IBD models. Beyond SCFA and IL‑10 pathways, these live biotherapeutic products suppress resident pathobionts and activate anti‑inflammatory AhR signaling via bacterial tryptophan metabolites, revealing IL‑10‑independent mechanisms of microbiome‑based therapy.

Gut microbiome diversity and composition differed across predefined age groups in a Taiwanese cohort. Several age‑associated genera showed partial agreement across complementary analytic methods. Adult gut microbiome profiles could predict chronological age, though only with modest accuracy, underscoring both biological signal and methodological limits.

Bacterial endosymbionts in Fusarium oxysporum enhance fungal virulence by reshaping the rhizosphere microbiome. Achromobacter spp. endosymbionts reduce disease‑suppressive bacteria, including Streptomyces, through beauvericin production. This tripartite interaction weakens microbiome‑based plant defense and intensifies pathogen impact.

Paired oral–fecal microbiomes from 507 individuals revealed elevated mouth‑to‑gut bacterial transmission in gastrointestinal cancers. A mouth‑to‑feces index captured disease‑specific signatures and powered a classifier that outperformed fecal occult blood testing, enabling sensitive, non‑invasive detection across multiple cohorts.

Gut microbes convert dietary nitrate and non‑heme iron into dinitrosyl iron complexes (DNICs) that circulate systemically and improve host metabolism. DNICs were detected in conventional but not germ‑free mice, and supplementation or synthetic DNICs boosted tissue levels and reduced cardiometabolic dysfunction. DNICs also lowered steatosis and normalized sGC‑mTORC1 signaling.

Structured RNA elements across the norovirus genome were mapped and functionally tested, revealing conserved motifs that regulate replication and translation. Disrupting key structures reduced viral fitness in cells and animals, enabling design of a stable attenuated virus that elicits protective immunity and supports RNA‑guided antiviral strategies.

A comprehensive proteomic analysis of Plasmodium falciparum chromatin identified 214 proteins associated with heterochromatin, euchromatin, and (peri)centromeric regions. Using three proximity-labeling methods, researchers uncovered new epigenetic factors, complexes involved in histone variant exchange and chromatin-RNA interactions, and evidence for a spindle assembly checkpoint previously thought absent.

Nipah virus (NiV) is a highly lethal zoonotic pathogen with significant pandemic potential due to its broad host range, cross-species transmission capacity, and ability to evade immune responses. This review examines NiV structure, pathogenesis, and the latest progress in vaccine development, highlighting promising candidates, key scientific challenges, knowledge gaps, and priorities for future prevention and control efforts.

Plant-microbe interactions are essential for sustainable agriculture, improving crop productivity, soil fertility, and resilience to stress. This review examines the role of plant growth-promoting microbes (PGPM) as biofertilizers and microbial inoculants, their mechanisms of action, factors influencing their effectiveness, and emerging technologies that support environmentally friendly farming and enhanced food security.

Mucin plays a key role in shaping interactions between enteropathogenic Yersinia enterocolitica and its mucus-adherent phage fMtkYen801. In vitro, mucin exposure increased phage replication by 100-fold, altered post-infection bacterial growth, and reduced biofilm formation. Resistant variants acquired mutations linked to virulence, quorum sensing, and antibiotic resistance, highlighting implications for phage therapy.

A 10-year study of 154 ocular MRSA isolates in Taiwan found major shifts in bacterial clones, with formerly dominant CC59 declining and fluoroquinolone-resistant CC8 increasing. While CC59 remained highly susceptible to fluoroquinolones, CC8 showed marked resistance, raising concerns about standard empirical treatment for eye infections and underscoring the need for ongoing molecular surveillance.

Lors de ma balade au Bois de Vincennes, j’ai vu ces champignons. L' IA pense qu’il s’agit d’un poulet-des-bois (Laetiporus spp.), mais avec seulement 80 % de certitude... donc 80 % de confiance aussi pour sa comestibilité. 🙃🍄

Using chemically induced  Effector-Triggered Immunity ( ETI) and single-cell transcriptomics in Arabidopsis leaves, researchers show that although pathogen effectors are broadly perceived, individual cell types mount distinct immune responses. A shared defense core is complemented by specialized programs shaped by cell identity and chromatin state. Epidermal regulators are crucial for preventing pathogen entry, revealing a layered, spatially organized plant immune system.

Scientists identified TgPRO, the first dedicated regulator of metabolic gene expression in apicomplexan parasites. In Toxoplasma gondii , TgPRO helps parasites adapt to crowding-induced oxidative stress by controlling genes involved in carbon metabolism and iron-sulfur cluster assembly. Loss of TgPRO increased reactive oxygen species and reduced fitness, revealing a convergently evolved metabolic control mechanism.

Researchers found that insoluble dietary fiber slows colorectal cancer progression in mice by altering gut microbiota and reducing production of the tumor-promoting ganglioside GM3. Fiber lowered levels of Paramuribaculum intestinale and a glycosphingolipid-related microbial enzyme, while GM3 was shown to stimulate tumor growth and inhibit cancer cell apoptosis.

Three Chlamydia species infect humans: C. trachomatis , C. pneumoniae and C. psittaci . C. trachomatis is the leading bacterial sexually transmitted infection, often asymptomatic but capable of causing pelvic inflammatory disease, infertility and neonatal infections. It also causes trachoma, a major source of preventable blindness. C. pneumoniae causes respiratory illnesses and may be linked to cardiovascular disease. Chlamydial infections occur worldwide, with trachoma concentrated in poorer regions. Globally, about 89 million new sexually transmitted cases arise annually.    

Many people who walk by Bastille don't realize that there's a pretty little alley a few meters from the crowded cafés.

Clouds are more than water droplets. They host active microbial communities and, potentially, vast numbers of viruses. This article explores evidence that the global cloud virome contains roughly 10²¹ virus particles, examines how virus-bacteria interactions may shape microbial ecology during atmospheric transport, and highlights key research priorities for understanding the ecological role of the cloud virosphere.

Age-linked loss of beneficial Lactobacillus and rise of L. iners impair endometrial receptivity and embryo transfer outcomes. L. gasseri and its exopollysaccharides (EPSs) counteract senescence, enhance implantation in aged mice, and act through Hippo‑YAP signaling, suggesting microbiome‑based strategies to improve fertility in older women.

Background The relationship between gastric microbiota composition, Helicobacter pylori infection, and eradication outcomes remains unclear. This study aims to explore the association of gastric microbiota composition among patients with refractory H. pylori infection with the outcomes of rescue therapy. Material and Methods Patients who failed to respond to second- or third-line eradication therapies were prospectively enrolled. The composition of the gastric microbiota was analyzed using 16S rRNA gene sequencing prior to rescue therapy. The eradication outcomes were confirmed using the [ 13 C]-urea breath test. Results Among 1,590 screened participants, 23 patients with refractory H. pylori infection who underwent rescue therapy based on antimicrobial susceptibility testing were enrolled. The alpha diversity did not differ between success and failure groups; however, the beta diversity analysis revealed a distinct microbial composition. The success group was enriched in Streptococ...

Metabolomics of single-strain & co-cultures of 7 Fusarium strains causing Fusarium head blight reveals metabolic modifications induced by strain co-occurrence. FHB metabolomics reveals species‑specific biomarkers & interaction‑driven shifts in co‑cultures.

Hadal microbes show distinct in situ activity, using refractory substrates & diverse electron acceptors to drive unique deep‑ocean biogeochemistry.